MATLAB Examples

Use the sbioconsmoiety function to find conserved quantities in a SimBiology® model.

Build, simulate and analyze a model in SimBiology® using a pathway taken from the literature.

Construct a simple model with two species (A and B) and a reaction. The reaction is A -> B, which follows the mass action kinetics with the forward rate parameter k. Hence the rate of change is .

In this example, you will use the parameter estimation capabilities of SimBiology™ to calculate F, the bioavailability, of the drug ondansetron. You will calculate F by fitting a model of

Perform a Monte Carlo simulation of a pharmacokinetic/pharmacodynamic (PK/PD) model for an antibacterial agent. This example is adapted from Katsube et al. [1] This example also shows how

Build a simple nonlinear mixed-effects model from clinical pharmacokinetic data.

Simulate and analyze a model in SimBiology® using a physiologically based model of the glucose-insulin system in normal and diabetic humans.

Correctly build a SimBiology® model that contains discontinuities.

Build and simulate a model using the SSA stochastic solver.

Build and simulate a model using the SSA stochastic solver and the Explicit Tau-Leaping solver.

Make ensemble runs and how to analyze the generated data in SimBiology®.

Perform a parameter scan by simulating a model multiple times, each time varying the value of a parameter.

Deploy a graphical application that simulates a SimBiology model. The example model is the Lotka-Volterra reaction system as described by Gillespie [1], which can be interpreted as a

Increase the amount or concentration of a species by a constant value using the zero-order rate rule. For example, suppose species x increases by a constant rate k . The rate of change is:

Change the amount of a species similar to a first-order reaction using the first-order rate rule. For example, suppose the species x decays exponentially. The rate of change of species x is:

Configure sbiofit to perform a hybrid optimization by first running the global solver particleswarm , followed by another minimization function, fmincon .

Create a rate rule where a species from one reaction can determine the rate of another reaction if it is in the second reaction rate equation. Similarly, a species from a reaction can determine

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